On ubuntu 12.04 with gnome-classic issuing a "window minimize" operation makes the GUI disappear forever (it's not in the minimized windows list). There's no way to get it back as it's not even in the notification area. I can only kill the process.
Dunno if it's related to #1522 -- I'm using current master branch: 6940626
The bug is really that the tray icon isn't there, because it was a configuration to "hide" the window when minimized.
So this is a duplicate of #1522